Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

  • value_type as 'ranked' since this provides a very robust analysis method.
  • intercation map as 'high confidence'
  • network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins
  • filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

    • Navigation/Query Panel:
    Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
    Rank Gene Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 3008 to 3057 of 66312 in total
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		Network Comparison Type
    		Interaction Map
    		red
    		green
    		network_comparison
    188 TPM1 tropomyosin 1 alpha chain (alpha-tropomyosin). [swissprot;acc:p09493] Rooted Subtracted Low confidence 70.7466 75.1547 4.4081
    189 ATP1B3 sodium/potassium-transporting atpase beta-3 chain (sodium/potassium- dependent atpase beta-3 subunit) (atpb-3). [swissprot;acc:p54709] Squared 52520.9 47400.8 5120.1
    CENPJ centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [refseq;acc:nm_018451] Divided 65169.1 58753.9 1.10919
    DCPS mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] High confidence 41502.9 30836.8 1.34589
    DGAT1 diacylglycerol o-acyltransferase 1 (ec 2.3.1.20) (diglyceride acyltransferase) (acat related gene product 1). [swissprot;acc:o75907] Rooted Low confidence 69.9065 74.2132 1.06161
    DNALI1 axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] Ranked 214.779 204.039 1.05264
    E2F2 transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] Rooted High confidence 46.0352 53.0192 1.15171
    GNAO1 guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] Subtracted 47.6504 36.9304 10.72
    NDUFA12 nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] Measured Low confidence 5811.84 6399.42 587.58
    NUBP2 nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] Rooted 69.7469 74.1228 4.3759
    PCYT1A cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585] Ranked High confidence 241.373 267.352 25.979
    PRMT8 protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] Measured 4366.44 5899.76 1533.32
    Ranked Divided 226.582 198.444 1.14179
    SFPQ splicing factor, proline-and glutamine-rich (polypyrimidine tract- binding protein-associated splicing factor) (ptb-associated splicing factor) (psf) (dna-binding p52/p100 complex, 100 kda subunit). [swissprot;acc:p23246] Squared Subtracted 70694.1 56989.9 13704.2
    SLC11A1 natural resistance-associated macrophage protein 1 (nramp 1). [swissprot;acc:p49279] Measured Divided Low confidence 6933.47 7456.24 1.0754
    STAMBPL1 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Ranked Subtracted 196.362 206.979 10.617
    STT3A oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Measured Divided High confidence 4571.89 5864.86 1.28281
    190 no value ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] Squared Low confidence 51507.8 46446.1 1.10898
    AQP4 aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087] High confidence 71389.9 96037.6 1.34525
    DDOST dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] Measured 4571.89 5864.86 1.28281
    FLAD1 fad synthetase. [refseq;acc:nm_025207] Ranked Subtracted 241.373 267.352 25.979
    FMO5 dimethylaniline monooxygenase [n-oxide forming] 5 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 5) (fmo 5) (dimethylaniline oxidase 5). [swissprot;acc:p49326] Divided Low confidence 210.557 200.074 1.0524
    Rooted 69.0062 73.256 1.06159
    GABARAP gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] High confidence 149.165 129.699 1.15009
    GNG11 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Ranked Subtracted Low confidence 211.383 221.976 10.593
    LIPF triacylglycerol lipase, gastric precursor (ec 3.1.1.3) (gastric lipase) (gl). [swissprot;acc:p07098] Squared 54309.4 49192.4 5117
    MAPK11 mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [swissprot;acc:p53778] High confidence 42411.6 55802.1 13390.5
    NCBP2L dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Rooted Low confidence 71.1262 75.4476 4.3214
    PHF12 phd finger protein 12; phd zinc finger transcription factor. [refseq;acc:nm_020889] Measured 10745.7 10160 585.7
    RAP1GAP rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] Rooted High confidence 47.6504 36.9304 10.72
    SNRP70 u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] Measured 4366.44 5899.76 1533.32
    Ranked Divided 226.582 198.444 1.14179
    TFDP2 transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] Measured Low confidence 6480.93 6966.05 1.07485
    191 no value bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340] Ranked Subtracted High confidence 241.373 267.352 25.979
    filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] Measured 4366.44 5899.76 1533.32
    Ranked Divided 226.582 198.444 1.14179
    AGBL3 similar to atp/gtp-binding protein. [sptrembl;acc:q8nem8] Measured Low confidence 9385.4 10086.4 1.07469
    AQP5 aquaporin 5. [swissprot;acc:p55064] Squared High confidence 71388.5 96035.2 1.34525
    ARAF a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] Rooted Subtracted 116.797 106.111 10.686
    CDC14C cdc14 homolog b isoform 2. [refseq;acc:nm_033331] Squared Low confidence 53433.9 48332.8 5101.1
    CYBB cytochrome b-245 heavy chain (p22 phagocyte b-cytochrome) (neutrophil cytochrome b, 91 kda polypeptide) (cgd91-phox) (gp91-phox) (heme binding membrane glycoprotein gp91phox) (cytochrome b(558) beta chain) (superoxide-generating nadph oxidase heavy chain subunit). [swissprot;acc:p04839] Rooted Divided 69.9165 74.2189 1.06154
    ICK intestinal cell kinase isoform a; mak-related kinase; serine/threonine protein kinase. [refseq;acc:nm_014920] Squared 45402.8 50350.5 1.10897
    PLDN pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] Rooted High confidence 63.1192 72.584 1.14995
    PXK px serine/threonine kinase. [refseq;acc:nm_017771] Ranked Subtracted Low confidence 196.372 206.947 10.575
    RAB37 ras-related protein rab-37. [swissprot;acc:q96ax2] Measured 10730.1 10148.2 581.9
    SF3B1 splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] Divided High confidence 4638.1 5923.4 1.27712
    SLC15A2 oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] Ranked Low confidence 201.43 191.43 1.05224
    SPHK1 sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1] Squared Subtracted High confidence 42411.6 55802.1 13390.5
    TPM4 tropomyosin alpha 4 chain (tropomyosin 4) (tm30p1). [swissprot;acc:p07226] Rooted Low confidence 70.8512 75.1709 4.3197
    192 no value bromodomain adjacent to zinc finger domain protein 1a (atp-utilizing chromatin assembly and remodeling factor 1) (hacf1) (atp-dependent chromatin remodelling protein) (williams syndrome transcription factor-related chromatin remodeling factor 180) (wcrf180) (hwalp1) (chrac subunit acf1) (hspc317). [swissprot;acc:q9nrl2] Ranked 196.372 206.947 10.575

    Legend:
    - Rank is the rank after comparing the two networks
    - Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
    - Hugo is the HGNC identifier if it exists
    - Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
    - Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
    - Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
    - Filtered specifies whether we only included the high confidence microarry measurements or not.
    - http://analysis.yellowcouch.org/